Source Code for Module Bio.GA.Selection.Abstract

 1  """Base selection class from which all Selectors should derive. 
 2  """ 
 3   
 4   
 5 -class AbstractSelection(object): 
 6      """Base class for Selector classes. 
 7   
 8      This classes provides useful functions for different selector classes 
 9      and also defines the functions that all selector classes must 
10      implement. 
11   
12      This class should not be used directly, but rather should be subclassed. 
13      """ 
14 -    def __init__(self, mutator, crossover, repairer = None): 
15          """Initialize a selector. 
16   
17          Arguments: 
18   
19          o mutator -- A Mutation object which will perform mutation 
20          on an individual. 
21   
22          o crossover -- A Crossover object which will take two 
23          individuals and produce two new individuals which may 
24          have had crossover occur. 
25   
26          o repairer -- A class which can do repair on rearranged genomes 
27          to eliminate infeasible individuals. If set at None, so repair 
28          will be done. 
29          """ 
30          self._mutator = mutator 
31          self._crossover = crossover 
32          self._repairer = repairer 
33   
34 -    def mutate_and_crossover(self, org_1, org_2): 
35          """Perform mutation and crossover on the two organisms. 
36   
37          This uses the classes mutator and crossover functions to 
38          perform the manipulations. 
39   
40          If a repair class is available, then the rearranged genomes will 
41          be repaired to make them feasible. 
42   
43          The newly created individuals are returned. 
44          """ 
45          # first crossover the two organisms 
46          cross_org_1, cross_org_2 = self._crossover.do_crossover(org_1, org_2) 
47   
48          # now perform mutation on the two organisms 
49          final_org_1 = self._mutator.mutate(cross_org_1) 
50          final_org_2 = self._mutator.mutate(cross_org_2) 
51   
52          # if we have a repair class, perform repair 
53          if self._repairer is not None: 
54              final_org_1 = self._repairer.repair(final_org_1) 
55              final_org_2 = self._repairer.repair(final_org_2) 
56   
57          return final_org_1, final_org_2 
58   
59 -    def select(self, population): 
60          raise NotImplementedError("Derived classes must implement.") 
61